JAL-3858 persist PAE matrix (only so far) as serialised floats in element on dataset...

[jalview.git] / src / jalview / project / Jalview2XML.java

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 4b9c348..2b1b687 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -89,6 +89,8 @@ import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ContactMatrix;
+import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.GeneLocus;
 import jalview.datamodel.GraphLine;
@@ -148,6 +150,7 @@ import jalview.viewmodel.ViewportRanges;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.dm.AAConSettings;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
@@ -192,6 +195,7 @@ import jalview.xml.binding.jalview.JalviewUserColours.Colour;
 import jalview.xml.binding.jalview.MapListType.MapListFrom;
 import jalview.xml.binding.jalview.MapListType.MapListTo;
 import jalview.xml.binding.jalview.Mapping;
+import jalview.xml.binding.jalview.MatrixType;
 import jalview.xml.binding.jalview.NoValueColour;
 import jalview.xml.binding.jalview.ObjectFactory;
 import jalview.xml.binding.jalview.PcaDataType;
@@ -1510,7 +1514,7 @@ public class Jalview2XML
                 ov.getCanvas().getResidueColour().getRGB());
         overview.setHiddenColour(ov.getCanvas().getHiddenColour().getRGB());
         view.setOverview(overview);
-      }
+      } 
       if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
       {
         view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
@@ -2289,6 +2293,22 @@ public class Jalview2XML
           line.setColour(annotation.getThreshold().colour.getRGB());
           an.setThresholdLine(line);
         }
+        if (annotation.graph==AlignmentAnnotation.CONTACT_MAP)
+        {
+          if (annotation.sequenceRef.getContactMaps()!=null)
+          {
+            ContactMatrixI cm = annotation.sequenceRef.getContactMatrixFor(annotation);
+            if (cm!=null)
+            {
+              MatrixType xmlmat = new MatrixType();
+              xmlmat.setType(cm.getType());
+              xmlmat.setRows(BigInteger.valueOf(cm.getWidth()));
+              xmlmat.setCols(BigInteger.valueOf(cm.getHeight()));
+              xmlmat.setValue(ContactMatrix.contactToFloatString(cm));
+              an.getContactmatrix().add(xmlmat);
+            }
+          }
+        }
       }
       else
       {
@@ -3902,6 +3922,40 @@ public class Jalview2XML
             jaa.setProperty(prop.getName(), prop.getValue());
           }
         }
+        if (jaa.graph == AlignmentAnnotation.CONTACT_MAP)
+        {
+          if (annotation.getContactmatrix() != null
+                  && annotation.getContactmatrix().size() > 0)
+          {
+            for (MatrixType xmlmat : annotation.getContactmatrix())
+            {
+              if (PAEContactMatrix.PAEMATRIX.equals(xmlmat.getType()))
+              {
+                if (!xmlmat.getRows().equals(xmlmat.getCols()))
+                {
+                  Console.error("Can't handle non square PAE Matrices");
+                }
+                else
+                {
+                  float[][] elements = ContactMatrix
+                          .fromFloatStringToContacts(xmlmat.getValue(),
+                                  xmlmat.getCols().intValue(),
+                                  xmlmat.getRows().intValue());
+
+                  PAEContactMatrix newpae = new PAEContactMatrix(
+                          jaa.sequenceRef, elements);
+                  jaa.sequenceRef.addContactListFor(jaa, newpae);
+                }
+              }
+              else
+              {
+                Console.error("Ignoring CONTACT_MAP annotation with type "
+                        + xmlmat.getType());
+              }
+            }
+          }
+        }
+
         if (jaa.autoCalculated)
         {
           autoAlan.add(new JvAnnotRow(i, jaa));
@@ -4122,7 +4176,7 @@ public class Jalview2XML
       loadPCAViewers(jalviewModel, ap);
       loadPDBStructures(jprovider, jseqs, af, ap);
       loadRnaViewers(jprovider, jseqs, ap);
-      loadOverview(view, af);
+      loadOverview(view, jalviewModel.getVersion(), af);
     }
     // and finally return.
     return af;
@@ -4135,8 +4189,13 @@ public class Jalview2XML
    * @param view
    * @param af
    */
-  protected void loadOverview(Viewport view, AlignFrame af)
+  protected void loadOverview(Viewport view, String version, AlignFrame af)
   {
+    if (!isVersionStringLaterThan("2.11.3",
+            version) && view.getOverview()==null)
+    {
+      return;
+    }
     /*
      * first close any Overview that was opened automatically
      * (if so configured in Preferences) so that the view is
@@ -4676,7 +4735,7 @@ public class Jalview2XML
    *          - minimum version we are comparing against
    * @param version
    *          - version of data being processsed
-   * @return
+   * @return true if version is equal to or later than supported
    */
   public static boolean isVersionStringLaterThan(String supported,
           String version)
@@ -5146,7 +5205,10 @@ public class Jalview2XML
               + annotationId);
       return null;
     }
-    if (matchedAnnotation.getThreshold() == null)
+    // belt-and-braces create a threshold line if the 
+    // colourscheme needs one but the matchedAnnotation doesn't have one
+    if (safeInt(viewAnnColour.getAboveThreshold()) != 0
+            && matchedAnnotation.getThreshold() == null)
     {
       matchedAnnotation.setThreshold(
               new GraphLine(safeFloat(viewAnnColour.getThreshold()),